Starting phenix.real_space_refine on Tue Jan 14 05:09:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bt8_44881/01_2025/9bt8_44881.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bt8_44881/01_2025/9bt8_44881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bt8_44881/01_2025/9bt8_44881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bt8_44881/01_2025/9bt8_44881.map" model { file = "/net/cci-nas-00/data/ceres_data/9bt8_44881/01_2025/9bt8_44881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bt8_44881/01_2025/9bt8_44881.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 16 5.16 5 C 3611 2.51 5 N 967 2.21 5 O 1112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 5712 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 439 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "H" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "V" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 120 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 849 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2596 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 21, 'TRANS': 304} Chain breaks: 3 Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Time building chain proxies: 4.22, per 1000 atoms: 0.74 Number of scatterers: 5712 At special positions: 0 Unit cell: (60.48, 122.4, 102.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 6 15.00 O 1112 8.00 N 967 7.00 C 3611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS B 120 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 668.3 milliseconds 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 14 sheets defined 4.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 90 through 94 removed outlier: 4.088A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.520A pdb=" N LYS A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'B' and resid 98 through 109 Processing sheet with id=AA1, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AA2, first strand: chain 'C' and resid 108 through 110 Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA4, first strand: chain 'H' and resid 61 through 63 removed outlier: 7.002A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N CYS H 99 " --> pdb=" O GLN H 115 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLN H 115 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ARG H 101 " --> pdb=" O TRP H 113 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TRP H 113 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'V' and resid 361 through 364 Processing sheet with id=AA6, first strand: chain 'A' and resid 4 through 7 removed outlier: 4.215A pdb=" N GLN A 5 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 23 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.532A pdb=" N THR A 111 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET A 34 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N SER A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.875A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.819A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.875A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.819A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 183 through 188 Processing sheet with id=AB2, first strand: chain 'B' and resid 207 through 208 removed outlier: 3.538A pdb=" N VAL B 343 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ALA B 239 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LYS B 250 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE B 241 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLN B 248 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.612A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.907A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 573 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1829 1.34 - 1.46: 1411 1.46 - 1.58: 2547 1.58 - 1.70: 22 1.70 - 1.82: 23 Bond restraints: 5832 Sorted by residual: bond pdb=" OG1 TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" OG1 TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" O3P TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" O2P TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O2P TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 1.528 1.608 -0.080 2.00e-02 2.50e+03 1.61e+01 ... (remaining 5827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 7839 2.53 - 5.06: 68 5.06 - 7.59: 8 7.59 - 10.12: 4 10.12 - 12.65: 2 Bond angle restraints: 7921 Sorted by residual: angle pdb=" CB TPO V 359 " pdb=" OG1 TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 119.31 106.66 12.65 3.00e+00 1.11e-01 1.78e+01 angle pdb=" CB TPO V 360 " pdb=" OG1 TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 119.31 107.34 11.97 3.00e+00 1.11e-01 1.59e+01 angle pdb=" OG1 TPO V 360 " pdb=" P TPO V 360 " pdb=" O1P TPO V 360 " ideal model delta sigma weight residual 100.43 109.72 -9.29 3.00e+00 1.11e-01 9.59e+00 angle pdb=" CA TYR B 63 " pdb=" C TYR B 63 " pdb=" O TYR B 63 " ideal model delta sigma weight residual 119.08 122.16 -3.08 1.03e+00 9.43e-01 8.96e+00 angle pdb=" OG1 TPO V 359 " pdb=" P TPO V 359 " pdb=" O1P TPO V 359 " ideal model delta sigma weight residual 100.43 109.32 -8.89 3.00e+00 1.11e-01 8.79e+00 ... (remaining 7916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 3016 17.83 - 35.66: 366 35.66 - 53.49: 78 53.49 - 71.32: 16 71.32 - 89.15: 6 Dihedral angle restraints: 3482 sinusoidal: 1367 harmonic: 2115 Sorted by residual: dihedral pdb=" CA VAL C 111 " pdb=" C VAL C 111 " pdb=" N ASN C 112 " pdb=" CA ASN C 112 " ideal model delta harmonic sigma weight residual -180.00 -158.42 -21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CB CYS C 95 " pdb=" SG CYS C 95 " pdb=" SG CYS B 120 " pdb=" CB CYS B 120 " ideal model delta sinusoidal sigma weight residual -86.00 -55.95 -30.05 1 1.00e+01 1.00e-02 1.29e+01 dihedral pdb=" CA LEU B 79 " pdb=" C LEU B 79 " pdb=" N PHE B 80 " pdb=" CA PHE B 80 " ideal model delta harmonic sigma weight residual 180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 3479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 516 0.029 - 0.058: 243 0.058 - 0.087: 67 0.087 - 0.116: 45 0.116 - 0.144: 22 Chirality restraints: 893 Sorted by residual: chirality pdb=" CB VAL C 111 " pdb=" CA VAL C 111 " pdb=" CG1 VAL C 111 " pdb=" CG2 VAL C 111 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA ILE L 49 " pdb=" N ILE L 49 " pdb=" C ILE L 49 " pdb=" CB ILE L 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ASP H 111 " pdb=" N ASP H 111 " pdb=" C ASP H 111 " pdb=" CB ASP H 111 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 890 not shown) Planarity restraints: 1000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 16 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO H 17 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO H 17 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 17 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 44 " 0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO B 45 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 45 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 45 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 107 " 0.006 2.00e-02 2.50e+03 1.22e-02 2.99e+00 pdb=" CG TYR H 107 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR H 107 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR H 107 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR H 107 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR H 107 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR H 107 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 107 " -0.006 2.00e-02 2.50e+03 ... (remaining 997 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1411 2.79 - 3.32: 4562 3.32 - 3.85: 8562 3.85 - 4.37: 9874 4.37 - 4.90: 18352 Nonbonded interactions: 42761 Sorted by model distance: nonbonded pdb=" OG SER H 36 " pdb=" O ILE H 54 " model vdw 2.269 3.040 nonbonded pdb=" OG SER B 13 " pdb=" OD1 ASN B 15 " model vdw 2.292 3.040 nonbonded pdb=" O ALA B 263 " pdb=" OG SER B 266 " model vdw 2.317 3.040 nonbonded pdb=" O SER H 66 " pdb=" NH2 ARG H 70 " model vdw 2.325 3.120 nonbonded pdb=" ND2 ASN C 135 " pdb=" O ARG B 76 " model vdw 2.328 3.120 ... (remaining 42756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.270 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 5832 Z= 0.296 Angle : 0.645 12.650 7921 Z= 0.318 Chirality : 0.043 0.144 893 Planarity : 0.005 0.066 1000 Dihedral : 16.428 89.153 2117 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.32 % Allowed : 25.44 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.32), residues: 700 helix: 1.19 (1.59), residues: 11 sheet: 0.48 (0.32), residues: 294 loop : -0.91 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.005 0.001 HIS C 122 PHE 0.012 0.001 PHE A 29 TYR 0.029 0.002 TYR H 107 ARG 0.007 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.659 Fit side-chains REVERT: H 107 TYR cc_start: 0.7548 (t80) cc_final: 0.7344 (t80) outliers start: 2 outliers final: 0 residues processed: 94 average time/residue: 0.2060 time to fit residues: 24.8673 Evaluate side-chains 91 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 18 optimal weight: 0.1980 chunk 35 optimal weight: 0.0980 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.117674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.097865 restraints weight = 7918.971| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.25 r_work: 0.3168 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5832 Z= 0.154 Angle : 0.531 8.478 7921 Z= 0.277 Chirality : 0.043 0.161 893 Planarity : 0.004 0.038 1000 Dihedral : 4.284 21.438 810 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.74 % Allowed : 24.80 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.32), residues: 700 helix: 1.83 (1.76), residues: 11 sheet: 0.81 (0.33), residues: 285 loop : -0.89 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.004 0.001 HIS C 122 PHE 0.013 0.001 PHE A 29 TYR 0.013 0.001 TYR C 90 ARG 0.002 0.000 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.604 Fit side-chains REVERT: B 110 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8092 (tm-30) REVERT: B 232 LYS cc_start: 0.8160 (mtpp) cc_final: 0.7881 (mttp) REVERT: L 80 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8054 (mt0) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 0.1926 time to fit residues: 25.8935 Evaluate side-chains 96 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 0.0020 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.5728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.097350 restraints weight = 7942.973| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.45 r_work: 0.2911 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5832 Z= 0.212 Angle : 0.534 8.675 7921 Z= 0.278 Chirality : 0.042 0.137 893 Planarity : 0.004 0.035 1000 Dihedral : 4.327 22.600 810 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.54 % Allowed : 25.12 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.32), residues: 700 helix: 1.53 (1.69), residues: 11 sheet: 0.79 (0.32), residues: 296 loop : -0.95 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.009 0.001 HIS C 122 PHE 0.012 0.001 PHE A 29 TYR 0.017 0.001 TYR C 136 ARG 0.003 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.626 Fit side-chains REVERT: H 107 TYR cc_start: 0.7358 (t80) cc_final: 0.6780 (t80) REVERT: B 110 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8008 (tm-30) REVERT: B 232 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7898 (mttt) REVERT: B 244 PHE cc_start: 0.8816 (m-10) cc_final: 0.8590 (m-10) REVERT: L 80 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7984 (mt0) outliers start: 22 outliers final: 16 residues processed: 107 average time/residue: 0.1933 time to fit residues: 26.6810 Evaluate side-chains 102 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 23 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS B 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.094587 restraints weight = 8135.208| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.47 r_work: 0.2973 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5832 Z= 0.323 Angle : 0.595 8.957 7921 Z= 0.310 Chirality : 0.044 0.138 893 Planarity : 0.004 0.044 1000 Dihedral : 4.637 20.399 810 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.48 % Allowed : 24.32 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.32), residues: 700 helix: 1.15 (1.69), residues: 11 sheet: 0.76 (0.32), residues: 296 loop : -1.09 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 50 HIS 0.011 0.001 HIS C 122 PHE 0.015 0.002 PHE H 105 TYR 0.024 0.002 TYR C 136 ARG 0.008 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.644 Fit side-chains REVERT: C 92 TYR cc_start: 0.8768 (t80) cc_final: 0.8527 (t80) REVERT: H 107 TYR cc_start: 0.7680 (t80) cc_final: 0.7244 (t80) REVERT: B 110 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7916 (tm-30) REVERT: B 232 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7768 (mttt) REVERT: B 244 PHE cc_start: 0.8855 (m-10) cc_final: 0.8522 (m-10) REVERT: L 80 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8132 (mt0) outliers start: 34 outliers final: 24 residues processed: 113 average time/residue: 0.1938 time to fit residues: 28.2553 Evaluate side-chains 108 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 1 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.117709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.096935 restraints weight = 7901.671| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.44 r_work: 0.2859 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5832 Z= 0.196 Angle : 0.526 8.555 7921 Z= 0.271 Chirality : 0.042 0.142 893 Planarity : 0.004 0.044 1000 Dihedral : 4.410 25.583 810 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.67 % Allowed : 25.60 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.31), residues: 700 helix: 1.20 (1.71), residues: 11 sheet: 0.85 (0.32), residues: 296 loop : -1.08 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.007 0.001 HIS C 122 PHE 0.013 0.001 PHE A 29 TYR 0.016 0.001 TYR C 136 ARG 0.009 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.597 Fit side-chains REVERT: C 92 TYR cc_start: 0.8812 (t80) cc_final: 0.8557 (t80) REVERT: H 107 TYR cc_start: 0.7392 (t80) cc_final: 0.6817 (t80) REVERT: B 110 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8017 (tm-30) REVERT: B 232 LYS cc_start: 0.8244 (mtpp) cc_final: 0.7856 (mttp) REVERT: B 244 PHE cc_start: 0.8814 (m-10) cc_final: 0.8584 (m-10) REVERT: L 80 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8009 (mt0) outliers start: 29 outliers final: 24 residues processed: 107 average time/residue: 0.2042 time to fit residues: 27.7891 Evaluate side-chains 106 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 3 optimal weight: 0.0170 chunk 52 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.097284 restraints weight = 7900.739| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.45 r_work: 0.3037 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5832 Z= 0.201 Angle : 0.527 8.596 7921 Z= 0.270 Chirality : 0.042 0.139 893 Planarity : 0.004 0.049 1000 Dihedral : 4.389 29.631 810 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.83 % Allowed : 26.89 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.32), residues: 700 helix: 1.23 (1.72), residues: 11 sheet: 0.86 (0.32), residues: 296 loop : -1.13 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.007 0.001 HIS C 122 PHE 0.013 0.001 PHE A 29 TYR 0.016 0.001 TYR C 136 ARG 0.010 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.660 Fit side-chains REVERT: C 92 TYR cc_start: 0.8832 (t80) cc_final: 0.8582 (t80) REVERT: H 107 TYR cc_start: 0.7372 (t80) cc_final: 0.6822 (t80) REVERT: B 110 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8085 (tm-30) REVERT: B 232 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7860 (mttt) REVERT: L 80 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7986 (mt0) outliers start: 30 outliers final: 26 residues processed: 108 average time/residue: 0.1891 time to fit residues: 26.3887 Evaluate side-chains 107 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.117790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.096700 restraints weight = 7893.849| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.45 r_work: 0.3000 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5832 Z= 0.237 Angle : 0.544 8.676 7921 Z= 0.281 Chirality : 0.043 0.177 893 Planarity : 0.004 0.054 1000 Dihedral : 4.486 32.000 810 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.48 % Allowed : 26.25 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.32), residues: 700 helix: 1.24 (1.72), residues: 11 sheet: 0.84 (0.32), residues: 296 loop : -1.17 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.007 0.001 HIS C 122 PHE 0.013 0.001 PHE A 29 TYR 0.018 0.001 TYR C 136 ARG 0.012 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 0.664 Fit side-chains REVERT: C 92 TYR cc_start: 0.8848 (t80) cc_final: 0.8605 (t80) REVERT: H 107 TYR cc_start: 0.7417 (t80) cc_final: 0.6874 (t80) REVERT: A 69 ILE cc_start: 0.8845 (tt) cc_final: 0.8620 (tt) REVERT: B 110 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7988 (tm-30) REVERT: B 232 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7878 (mttt) REVERT: L 80 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7969 (mt0) outliers start: 34 outliers final: 27 residues processed: 110 average time/residue: 0.2156 time to fit residues: 29.9691 Evaluate side-chains 111 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 56 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.114795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.093723 restraints weight = 7965.536| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.44 r_work: 0.3026 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 5832 Z= 0.423 Angle : 0.664 10.530 7921 Z= 0.343 Chirality : 0.047 0.169 893 Planarity : 0.005 0.060 1000 Dihedral : 5.092 33.260 810 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.31 % Allowed : 26.73 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.32), residues: 700 helix: 1.16 (1.72), residues: 11 sheet: 0.74 (0.33), residues: 284 loop : -1.32 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 50 HIS 0.009 0.001 HIS C 122 PHE 0.019 0.002 PHE H 105 TYR 0.025 0.002 TYR C 136 ARG 0.012 0.001 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 84 time to evaluate : 0.647 Fit side-chains REVERT: H 107 TYR cc_start: 0.7854 (t80) cc_final: 0.7489 (t80) REVERT: A 43 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8190 (mtpp) REVERT: B 110 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8061 (tm-30) REVERT: B 232 LYS cc_start: 0.8288 (mtpp) cc_final: 0.7931 (mttt) REVERT: L 80 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8174 (mt0) outliers start: 33 outliers final: 26 residues processed: 112 average time/residue: 0.1841 time to fit residues: 26.7251 Evaluate side-chains 109 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.094764 restraints weight = 7871.415| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.46 r_work: 0.3041 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5832 Z= 0.224 Angle : 0.554 8.621 7921 Z= 0.285 Chirality : 0.043 0.215 893 Planarity : 0.004 0.062 1000 Dihedral : 4.834 41.244 810 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.67 % Allowed : 27.86 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.32), residues: 700 helix: 1.25 (1.73), residues: 11 sheet: 0.76 (0.32), residues: 296 loop : -1.25 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.007 0.001 HIS C 122 PHE 0.014 0.001 PHE A 29 TYR 0.019 0.001 TYR B 63 ARG 0.013 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.706 Fit side-chains REVERT: H 107 TYR cc_start: 0.7613 (t80) cc_final: 0.7188 (t80) REVERT: A 43 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8214 (mtpp) REVERT: B 110 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8115 (tm-30) REVERT: B 232 LYS cc_start: 0.8279 (mtpp) cc_final: 0.7945 (mttt) REVERT: L 80 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7993 (mt0) outliers start: 29 outliers final: 27 residues processed: 108 average time/residue: 0.2035 time to fit residues: 28.5609 Evaluate side-chains 110 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 0.0000 chunk 25 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.0570 chunk 67 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.120523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.099339 restraints weight = 7922.891| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.47 r_work: 0.2950 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5832 Z= 0.160 Angle : 0.517 8.558 7921 Z= 0.264 Chirality : 0.042 0.170 893 Planarity : 0.004 0.064 1000 Dihedral : 4.653 50.026 810 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.03 % Allowed : 28.66 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.31), residues: 700 helix: 1.27 (1.71), residues: 11 sheet: 0.85 (0.32), residues: 296 loop : -1.20 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.006 0.001 HIS C 122 PHE 0.013 0.001 PHE A 29 TYR 0.018 0.001 TYR B 63 ARG 0.015 0.000 ARG L 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.612 Fit side-chains REVERT: H 107 TYR cc_start: 0.7369 (t80) cc_final: 0.6811 (t80) REVERT: A 43 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8441 (mtpp) REVERT: B 110 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8097 (tm-30) REVERT: B 232 LYS cc_start: 0.8278 (mtpp) cc_final: 0.7971 (mttt) REVERT: L 80 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7821 (mt0) outliers start: 25 outliers final: 21 residues processed: 103 average time/residue: 0.1937 time to fit residues: 25.7410 Evaluate side-chains 105 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 0.0370 chunk 10 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.119241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.098096 restraints weight = 7985.001| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.48 r_work: 0.3037 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5832 Z= 0.200 Angle : 0.540 8.598 7921 Z= 0.276 Chirality : 0.042 0.151 893 Planarity : 0.004 0.062 1000 Dihedral : 4.796 53.088 810 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.19 % Allowed : 28.34 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.31), residues: 700 helix: 1.33 (1.73), residues: 11 sheet: 0.80 (0.31), residues: 298 loop : -1.19 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.011 0.001 HIS C 122 PHE 0.013 0.001 PHE A 29 TYR 0.017 0.001 TYR B 63 ARG 0.013 0.000 ARG L 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3008.04 seconds wall clock time: 55 minutes 13.08 seconds (3313.08 seconds total)